Research workbench
Structure of unliganded HSV gd reveals a mechanism for receptor- mediated activation of virus entry
Analyse Structure of unliganded HSV gd reveals a mechanism for receptor- mediated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C3A
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein D
- UniProt
- P57083
- Ligands
- NAG, ZN, NA, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein D | protein | 252 | 13% helix, 31% strand | P57083 |
| B | Glycoprotein D | protein | 274 | 11% helix, 28% strand | P57083 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.73 | 0.89 | 43 | empty |
| 2 | 79 | 0.35 | 0.76 | 20 | empty |
| 3 | 53 | 0.28 | 0.75 | 14 | empty |
| 4 | 62 | 0.27 | 0.73 | 15 | empty |
| 5 | 52 | 0.26 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 994 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2C3A · Structure of unliganded HSV gD reveals a mechanism for receptor- mediated activation of… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P57083
- Elsewhere: RCSB PDB 2C3A · PDBe 2C3A · UniProt P57083
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